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@zhongwulai and all;
@ohofmann ran into a variant calling case where VarDict appears to be missing a real indel. Running FreeBayes on the same region results in a deletion call with high depth and a c…
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I have seen the following exit message on error:
Exception in thread "main" java.lang.StringIndexOutOfBoundsException: String index out of range: -1
at java.lang.String.charAt(String.java:658)
at com…
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This produces an error (used -k 0 to turn off local realignment):
VarDict -G human_g1k_v37_decoy.fasta -f 0.01 -h -b 'tumor.k.bam|normal.k.bam' -k 0 -Q 1 -c 1 -S 2 -E 3 -g 4 1.k.bed
The error message…
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Hi,
I am trying to create an index for drop seq experiments using STAR. To fine tune our drop seq setup we need to have a mixture of human and mouse cell lines. Drop seq provides a meta fasta and gtf …
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We've been testing VarDictJava on whole genome analyses chunked into analyzable sections. We typically break up the genome at natural breakpoints without coverage to avoid accidentally splitting an an…
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Error when reading Gaussian files with HPModes frequencies. filetypes.py checks for the presence of "Haromic" two places, obvious misspelling. Does this mean no one has used the HPModes keyword? We sh…
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Hi there,
Thanks for Manta, it's a great tool. I'm at a loss with one of my samples:
```
[2016-02-15T15:32:06.556814] [chara.usbod.astrazeneca.net] [26339_1] [WorkflowRunner] Adding command task 'gen…
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When running with -mgeig with multiple pairs, I get the error "ValueError: matrices are not aligned", it would be very helpful to also get the output about WHICH pair this is for. Now I have to run al…
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I would like to run Vardict on total RNA data, allowing for variants to be called anywhere they are observed along the chromosome. I have tried breaking the chromosome into 6 segments (by bed) and ru…
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Is there any driver script to easily run vardict on a human WGS tumor-normal pair?
Due to memory requirements, it is not possible to run it on the whole genome. Even splitting by chromosome is not en…